Variant report

Variant	rs7699226
Chromosome Location	chr4:85877561-85877562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:85876909..85884375-chr4:85886007..85890757,11	MCF-7	breast:
2	chr4:85877154..85880144-chr4:85883390..85884959,2	MCF-7	breast:
3	chr4:85871120..85875052-chr4:85876385..85879344,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180769	Chromatin interaction
ENSG00000163625	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10029496	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10856851	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10856852	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs11097026	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11097028	0.82[EUR][1000 genomes]
rs11730981	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732309	0.89[EUR][1000 genomes]
rs11732347	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12498637	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12498787	0.88[EUR][1000 genomes]
rs12502559	0.81[EUR][1000 genomes]
rs12503215	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12506456	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12510410	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12640378	0.87[EUR][1000 genomes]
rs12648852	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13109918	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13114115	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13118671	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs13124246	0.90[EUR][1000 genomes]
rs13125323	0.81[EUR][1000 genomes]
rs13141322	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13148035	0.89[EUR][1000 genomes]
rs1508670	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs17009317	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs17009334	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs17009341	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2046402	0.81[AMR][1000 genomes]
rs2046404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869216	1.00[ASW][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs28754901	0.92[EUR][1000 genomes]
rs3098928	0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]
rs34239067	0.87[EUR][1000 genomes]
rs34314581	0.90[EUR][1000 genomes]
rs4131745	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4376130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383611	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4464556	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470615	0.86[EUR][1000 genomes]
rs4533765	0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4590017	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4624645	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4626191	0.88[EUR][1000 genomes]
rs4634212	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55871210	0.82[EUR][1000 genomes]
rs56194765	0.89[EUR][1000 genomes]
rs58074983	0.82[EUR][1000 genomes]
rs6531777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6531782	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6531783	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs67045782	0.83[AMR][1000 genomes]
rs67624868	0.82[EUR][1000 genomes]
rs6815917	0.81[EUR][1000 genomes]
rs6820517	0.82[EUR][1000 genomes]
rs6833661	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6835046	0.86[AMR][1000 genomes]
rs6847067	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6847564	0.81[JPT][hapmap]
rs6847811	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857555	0.82[AMR][1000 genomes]
rs6858666	0.82[CHB][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]
rs71597394	0.81[EUR][1000 genomes]
rs72664952	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7654035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663580	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs7675324	0.88[EUR][1000 genomes]
rs7682896	0.81[EUR][1000 genomes]
rs7685537	0.86[JPT][hapmap];0.96[MEX][hapmap]
rs7692223	0.86[JPT][hapmap]
rs7694949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684737	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9790649	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv508295	chr4:85822802-85885027	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv879516	chr4:85877561-85895436	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7699226	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85845600-85882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:85865200-85886400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:85865800-85885400	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:85866000-85886200	Weak transcription	Fetal Intestine Small	intestine
5	chr4:85866400-85879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:85866800-85884600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:85867800-85878600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:85869600-85879800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:85869800-85879200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:85870200-85879200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:85870400-85879200	Weak transcription	Adipose Nuclei	Adipose
12	chr4:85870400-85880800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr4:85871000-85879200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:85872000-85886600	Weak transcription	Lung	lung
15	chr4:85873200-85877600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:85873200-85879200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:85873200-85879200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:85873400-85878600	Weak transcription	Stomach Mucosa	stomach
19	chr4:85873400-85879200	Weak transcription	Pancreas	Pancrea
20	chr4:85873400-85879600	Weak transcription	Gastric	stomach
21	chr4:85873400-85886600	Weak transcription	Esophagus	oesophagus
22	chr4:85873600-85878600	Weak transcription	Liver	Liver
23	chr4:85873800-85878800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:85873800-85879000	Weak transcription	NH-A	brain
25	chr4:85873800-85880600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:85873800-85884800	Weak transcription	HSMM	muscle
27	chr4:85873800-85885400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:85873800-85885800	Weak transcription	Osteobl	bone
29	chr4:85874000-85884600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:85874200-85879200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:85874400-85878600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:85874600-85878600	Weak transcription	NHDF-Ad	bronchial
33	chr4:85874600-85879400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:85874600-85886200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:85875000-85878000	Enhancers	Brain Angular Gyrus	brain
36	chr4:85875000-85880000	Enhancers	Brain Cingulate Gyrus	brain
37	chr4:85875200-85877600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr4:85875200-85877600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr4:85875200-85878000	Enhancers	Brain Substantia Nigra	brain
40	chr4:85875200-85878600	Weak transcription	Fetal Intestine Large	intestine
41	chr4:85875200-85881600	Enhancers	Brain Anterior Caudate	brain
42	chr4:85875800-85877600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr4:85875800-85877600	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr4:85875800-85877600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:85876000-85877600	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr4:85876000-85877600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr4:85876000-85877600	Enhancers	Colon Smooth Muscle	Colon
48	chr4:85876000-85882000	Enhancers	Brain Hippocampus Middle	brain
49	chr4:85876400-85877600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:85876400-85878000	Enhancers	Fetal Heart	heart

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